WebApollo: A Web-based Sequence Annotation Editor for Distributed Community Annotation

As genome sequencing becomes more efficient, annotation efforts must adapt to keep pace. With a
larger reliance on contributions from domain specialists, the curation environment is shifting from a
traditional centralized model to a geographically dispersed community annotation model—which requires
new tools to support collaborative annotation. WebApollo is a successor to the original Apollo annotation
editor and provides a web-based environment that allows multiple distributed users to edit and share
sequence annotations. The WebApollo client is designed as an extension to JBrowse, a genome browser
that provides a fast, highly interactive interface for visualizing genomic data. WebApollo allows users to
create and modify transcript and exon structure via intuitive gestures, and also flags potential problems
within these curated annotations. A server data broker allows dynamic access to genomic analyses
results from both UCSC and Chado genome databases, and client code provides direct access to BAM
data files to enable deep sequencing visualization. A server annotation editing engine handles edit logic
and deals with the complexities of modifications in a biological context, where a single change can have
multiple cascading effects (e.g., when splitting or merging transcripts). All edits are automatically stored
persistently in the server, which ensures reliability and allows the client to show edit histories and provide
full undo and redo functions. The server provides synchronized updates over multiple browser instances,
so annotation edits are immediately visible to all users who are working on the same region. Additional
information and code are available at http://gmod.org/wiki/WebApollo.

Public demo: http://icebox.lbl.gov:8080/WebApolloDemo